Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.
☆29Nov 1, 2025Updated 5 months ago
Alternatives and similar repositories for clusttraj
Users that are interested in clusttraj are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- open toolbox for structural comparison☆13Dec 13, 2018Updated 7 years ago
- Quantum machine learning (QML) molecular representations and core functions☆25Feb 21, 2026Updated last month
- Compare molecular structures after energy minimization in various force fields.☆10Aug 22, 2020Updated 5 years ago
- A python implementation of pdb2oniom for QM/MM (ONIOM) calculations☆11Oct 2, 2025Updated 6 months ago
- FragIt main repository☆27Mar 6, 2026Updated last month
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- Python script to lookup pKa values☆26Mar 31, 2026Updated 2 weeks ago
- Bondorder and formal charge determination for molecules☆10Jan 16, 2022Updated 4 years ago
- A quick tutorial for modern materials science, should the reader be not familiar with it and just wishing to crack the data☆16Aug 24, 2025Updated 7 months ago
- pyRMSD is a small Python package that aims to offer an integrative and efficient way of performing RMSD calculations of large sets of str…☆28Aug 20, 2020Updated 5 years ago
- Gromacs molecular dynamics simulation analysis scripts☆10Apr 5, 2022Updated 4 years ago
- Repo hosting the MetFrag website☆10Apr 6, 2026Updated last week
- OCEAN - Optimized Cross rEActivity estimatioN☆12Apr 29, 2020Updated 5 years ago
- MolEnc: a molecular encoder using rdkit and OCaml.☆21Mar 10, 2026Updated last month
- ☆11Jan 23, 2019Updated 7 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- A geometry-complete diffusion generative model (GCDM) for structure-based drug design (Nature CommsChem)☆24Nov 6, 2024Updated last year
- Solv@TUM - The Solvation Free Energy Database☆13Mar 31, 2024Updated 2 years ago
- ☆13Sep 4, 2021Updated 4 years ago
- A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations☆13Feb 20, 2023Updated 3 years ago
- Generator of polynomial machine learning potentials☆20Apr 8, 2026Updated last week
- Analysis and design of protein-protein or protein-peptide interactions based on atlas database.☆15Sep 27, 2022Updated 3 years ago
- Genarris is a random molecular crystal structure generator.☆30Mar 27, 2026Updated 2 weeks ago
- This module includes functions that can be used to simulate mechanochemical phenomena.☆11Nov 16, 2021Updated 4 years ago
- Rank binders by structure modeling☆16Updated this week
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"☆22Oct 2, 2024Updated last year
- ☆40Feb 26, 2023Updated 3 years ago
- Modeling framework for eTRANSAFE project☆13Aug 6, 2025Updated 8 months ago
- ☆19Jul 14, 2022Updated 3 years ago
- Python code for Hückel and Pariser-Parr-Pople molecular orbital theory☆15Aug 28, 2023Updated 2 years ago
- A library to align rigid molecules and clusters☆12Mar 17, 2026Updated 3 weeks ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Jan 16, 2015Updated 11 years ago
- A stripped-down set of just antechamber, sqm, and tleap.☆34Sep 20, 2021Updated 4 years ago
- mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data☆40Mar 19, 2026Updated 3 weeks ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆46Nov 25, 2025Updated 4 months ago
- Subset of AmberTools, with updates and modifications☆16Updated this week
- Optimization tool for calibrating coarse-grained force fields of lipids, relying on the simultaneous usage of reference AA trajectories (…☆10Jun 6, 2023Updated 2 years ago
- VMD Plugin and associated scripts to build lignin structures from topological specifications☆17Jul 17, 2025Updated 8 months ago
- This is the public repository for the RING PyMOL plugin developed by the BioComputing UP laboratory at the University of Padua☆31Sep 17, 2025Updated 6 months ago
- Euphonic is a Python package for efficient simulation of phonon bandstructures, density of states and inelastic neutron scattering intens…☆41Apr 8, 2026Updated last week
- machine learning interatomic potentials aiida plugin☆24Apr 7, 2026Updated last week